@jbrowse/plugin-sequence 2.0.0 → 2.1.2

package/dist/{referenceSeqTrackConfig.js → ReferenceSequenceTrack/configSchema.js}

@@ -1,20 +1,9 @@
 "use strict";
-var __assign = (this && this.__assign) || function () {
-    __assign = Object.assign || function(t) {
-        for (var s, i = 1, n = arguments.length; i < n; i++) {
-            s = arguments[i];
-            for (var p in s) if (Object.prototype.hasOwnProperty.call(s, p))
-                t[p] = s[p];
-        }
-        return t;
-    };
-    return __assign.apply(this, arguments);
-};
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.createReferenceSeqTrackConfig = void 0;
 /* eslint-disable @typescript-eslint/no-explicit-any */
-var mobx_state_tree_1 = require("mobx-state-tree");
-var configuration_1 = require("@jbrowse/core/configuration");
+const mobx_state_tree_1 = require("mobx-state-tree");
+const configuration_1 = require("@jbrowse/core/configuration");
 /*
 Note: this is primarily a copy of createBaseTrackConfig, except with a subset
 of the config slots, to avoid including fields that don't make sense for the
@@ -35,44 +24,44 @@ function createReferenceSeqTrackConfig(pluginManager) {
             defaultValue: {},
         },
     }, {
-        preProcessSnapshot: function (s) {
-            var snap = JSON.parse(JSON.stringify(s));
-            var displayTypes = new Set();
-            var _a = snap.displays, displays = _a === void 0 ? [] : _a;
+        preProcessSnapshot: s => {
+            const snap = JSON.parse(JSON.stringify(s));
+            const displayTypes = new Set();
+            const { displays = [] } = snap;
             if (snap.trackId !== 'placeholderId') {
                 // Gets the displays on the track snapshot and the possible displays
                 // from the track type and adds any missing possible displays to the
                 // snapshot
-                displays.forEach(function (d) { return d && displayTypes.add(d.type); });
-                var trackType = pluginManager.getTrackType(snap.type);
-                trackType.displayTypes.forEach(function (displayType) {
+                displays.forEach((d) => d && displayTypes.add(d.type));
+                const trackType = pluginManager.getTrackType(snap.type);
+                trackType.displayTypes.forEach(displayType => {
                     if (!displayTypes.has(displayType.name)) {
                         displays.push({
-                            displayId: "".concat(snap.trackId, "-").concat(displayType.name),
+                            displayId: `${snap.trackId}-${displayType.name}`,
                             type: displayType.name,
                         });
                     }
                 });
             }
-            return __assign(__assign({}, snap), { displays: displays });
+            return { ...snap, displays };
         },
         explicitIdentifier: 'trackId',
         explicitlyTyped: true,
-        actions: function (self) { return ({
-            addDisplayConf: function (displayConf) {
-                var type = displayConf.type;
+        actions: (self) => ({
+            addDisplayConf(displayConf) {
+                const { type } = displayConf;
                 if (!type) {
-                    throw new Error("unknown display type ".concat(type));
+                    throw new Error(`unknown display type ${type}`);
                 }
-                var display = self.displays.find(function (d) { return d && d.displayId === displayConf.displayId; });
+                const display = self.displays.find((d) => d && d.displayId === displayConf.displayId);
                 if (display) {
                     return display;
                 }
-                var length = self.displays.push(displayConf);
+                const length = self.displays.push(displayConf);
                 return self.displays[length - 1];
             },
-        }); },
+        }),
     });
 }
 exports.createReferenceSeqTrackConfig = createReferenceSeqTrackConfig;
-//# sourceMappingURL=referenceSeqTrackConfig.js.map
+//# sourceMappingURL=configSchema.js.map

package/dist/ReferenceSequenceTrack/configSchema.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/ReferenceSequenceTrack/configSchema.ts"],"names":[],"mappings":";;;AAAA,uDAAuD;AACvD,qDAAuC;AACvC,+DAAiE;AAGjE;;;;EAIE;AACF,SAAgB,6BAA6B,CAAC,aAA4B;IACxE,OAAO,IAAA,mCAAmB,EACxB,wBAAwB,EACxB;QACE,OAAO,EAAE,aAAa,CAAC,yBAAyB,CAAC,SAAS,CAAC;QAC3D,QAAQ,EAAE,uBAAK,CAAC,KAAK,CAAC,aAAa,CAAC,yBAAyB,CAAC,SAAS,CAAC,CAAC;QACzE,IAAI,EAAE;YACJ,IAAI,EAAE,QAAQ;YACd,WAAW,EAAE,qBAAqB;YAClC,YAAY,EAAE,EAAE;SACjB;QACD,QAAQ,EAAE;YACR,IAAI,EAAE,QAAQ;YACd,WAAW,EAAE,kCAAkC;YAC/C,YAAY,EAAE,EAAE;SACjB;KACF,EACD;QACE,kBAAkB,EAAE,CAAC,CAAC,EAAE;YACtB,MAAM,IAAI,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC,CAAA;YAC1C,MAAM,YAAY,GAAG,IAAI,GAAG,EAAE,CAAA;YAC9B,MAAM,EAAE,QAAQ,GAAG,EAAE,EAAE,GAAG,IAAI,CAAA;YAC9B,IAAI,IAAI,CAAC,OAAO,KAAK,eAAe,EAAE;gBACpC,oEAAoE;gBACpE,oEAAoE;gBACpE,WAAW;gBACX,QAAQ,CAAC,OAAO,CAAC,CAAC,CAAM,EAAE,EAAE,CAAC,CAAC,IAAI,YAAY,CAAC,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAA;gBAC3D,MAAM,SAAS,GAAG,aAAa,CAAC,YAAY,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;gBACvD,SAAS,CAAC,YAAY,CAAC,OAAO,CAAC,WAAW,CAAC,EAAE;oBAC3C,IAAI,CAAC,YAAY,CAAC,GAAG,CAAC,WAAW,CAAC,IAAI,CAAC,EAAE;wBACvC,QAAQ,CAAC,IAAI,CAAC;4BACZ,SAAS,EAAE,GAAG,IAAI,CAAC,OAAO,IAAI,WAAW,CAAC,IAAI,EAAE;4BAChD,IAAI,EAAE,WAAW,CAAC,IAAI;yBACvB,CAAC,CAAA;qBACH;gBACH,CAAC,CAAC,CAAA;aACH;YACD,OAAO,EAAE,GAAG,IAAI,EAAE,QAAQ,EAAE,CAAA;QAC9B,CAAC;QACD,kBAAkB,EAAE,SAAS;QAC7B,eAAe,EAAE,IAAI;QACrB,OAAO,EAAE,CAAC,IAAS,EAAE,EAAE,CAAC,CAAC;YACvB,cAAc,CAAC,WAAgD;gBAC7D,MAAM,EAAE,IAAI,EAAE,GAAG,WAAW,CAAA;gBAC5B,IAAI,CAAC,IAAI,EAAE;oBACT,MAAM,IAAI,KAAK,CAAC,wBAAwB,IAAI,EAAE,CAAC,CAAA;iBAChD;gBACD,MAAM,OAAO,GAAG,IAAI,CAAC,QAAQ,CAAC,IAAI,CAChC,CAAC,CAAM,EAAE,EAAE,CAAC,CAAC,IAAI,CAAC,CAAC,SAAS,KAAK,WAAW,CAAC,SAAS,CACvD,CAAA;gBACD,IAAI,OAAO,EAAE;oBACX,OAAO,OAAO,CAAA;iBACf;gBACD,MAAM,MAAM,GAAG,IAAI,CAAC,QAAQ,CAAC,IAAI,CAAC,WAAW,CAAC,CAAA;gBAC9C,OAAO,IAAI,CAAC,QAAQ,CAAC,MAAM,GAAG,CAAC,CAAC,CAAA;YAClC,CAAC;SACF,CAAC;KACH,CACF,CAAA;AACH,CAAC;AA3DD,sEA2DC"}

package/dist/ReferenceSequenceTrack/index.d.ts

@@ -0,0 +1,3 @@
+import PluginManager from '@jbrowse/core/PluginManager';
+declare const _default: (pluginManager: PluginManager) => void;
+export default _default;

package/dist/ReferenceSequenceTrack/index.js

@@ -0,0 +1,19 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+const TrackType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/TrackType"));
+const models_1 = require("@jbrowse/core/pluggableElementTypes/models");
+const configSchema_1 = require("./configSchema");
+exports.default = (pluginManager) => {
+    pluginManager.addTrackType(() => {
+        const configSchema = (0, configSchema_1.createReferenceSeqTrackConfig)(pluginManager);
+        return new TrackType_1.default({
+            name: 'ReferenceSequenceTrack',
+            configSchema,
+            stateModel: (0, models_1.createBaseTrackModel)(pluginManager, 'ReferenceSequenceTrack', configSchema),
+        });
+    });
+};
+//# sourceMappingURL=index.js.map

package/dist/ReferenceSequenceTrack/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/ReferenceSequenceTrack/index.ts"],"names":[],"mappings":";;;;;AAEA,8FAAqE;AACrE,uEAAiF;AACjF,iDAA8D;AAE9D,kBAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,YAAY,CAAC,GAAG,EAAE;QAC9B,MAAM,YAAY,GAAG,IAAA,4CAA6B,EAAC,aAAa,CAAC,CAAA;QAEjE,OAAO,IAAI,mBAAS,CAAC;YACnB,IAAI,EAAE,wBAAwB;YAC9B,YAAY;YACZ,UAAU,EAAE,IAAA,6BAAoB,EAC9B,aAAa,EACb,wBAAwB,EACxB,YAAY,CACb;SACF,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC,CAAA"}

package/dist/SequenceSearchAdapter/SequenceSearchAdapter.d.ts

@@ -0,0 +1,8 @@
+import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { Feature, Region } from '@jbrowse/core/util';
+export default class extends BaseFeatureDataAdapter {
+    configure(): Promise<BaseFeatureDataAdapter>;
+    getRefNames(): Promise<string[]>;
+    getFeatures(query: Region, opts: BaseOptions): import("rxjs").Observable<Feature>;
+    freeResources(): void;
+}

package/dist/SequenceSearchAdapter/SequenceSearchAdapter.js

@@ -0,0 +1,84 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+const BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
+const rxjs_1 = require("@jbrowse/core/util/rxjs");
+const util_1 = require("@jbrowse/core/util");
+const operators_1 = require("rxjs/operators");
+class default_1 extends BaseAdapter_1.BaseFeatureDataAdapter {
+    async configure() {
+        var _a;
+        const adapter = await ((_a = this.getSubAdapter) === null || _a === void 0 ? void 0 : _a.call(this, this.getConf('sequenceAdapter')));
+        if (!adapter) {
+            throw new Error('Error getting subadapter');
+        }
+        return adapter.dataAdapter;
+    }
+    async getRefNames() {
+        const adapter = await this.configure();
+        return adapter.getRefNames();
+    }
+    getFeatures(query, opts) {
+        return (0, rxjs_1.ObservableCreate)(async (observer) => {
+            var _a;
+            const sequenceAdapter = await this.configure();
+            const hw = 1000;
+            let { start: queryStart, end: queryEnd } = query;
+            queryStart = Math.max(0, queryStart - hw);
+            queryEnd += hw;
+            if (queryEnd < 0 || queryStart > queryEnd) {
+                observer.complete();
+                return;
+            }
+            const ret = sequenceAdapter.getFeatures({
+                ...query,
+                start: queryStart,
+                end: queryEnd,
+            }, opts);
+            const feats = await ret.pipe((0, operators_1.toArray)()).toPromise();
+            const residues = ((_a = feats[0]) === null || _a === void 0 ? void 0 : _a.get('seq')) || '';
+            const search = this.getConf('search');
+            const searchFoward = this.getConf('searchForward');
+            const searchReverse = this.getConf('searchReverse');
+            const caseInsensitive = this.getConf('caseInsensitive');
+            const re = new RegExp(search, 'g' + (caseInsensitive ? 'i' : ''));
+            if (search) {
+                if (searchFoward) {
+                    const matches = residues.matchAll(re);
+                    for (const match of matches) {
+                        const s = queryStart + (match.index || 0);
+                        if ((0, util_1.doesIntersect2)(s, s + search.length, query.start, query.end)) {
+                            observer.next(new util_1.SimpleFeature({
+                                uniqueId: `${this.id}-match-${s}-p`,
+                                refName: query.refName,
+                                start: s,
+                                end: s + match[0].length,
+                                name: match[0],
+                                strand: 1,
+                            }));
+                        }
+                    }
+                }
+                if (searchReverse) {
+                    const matches = (0, util_1.revcom)(residues).matchAll(re);
+                    for (const match of matches) {
+                        const s = queryEnd - (match.index || 0);
+                        if ((0, util_1.doesIntersect2)(s, s + search.length, query.start, query.end)) {
+                            observer.next(new util_1.SimpleFeature({
+                                uniqueId: `${this.id}-match-${s}-n`,
+                                refName: query.refName,
+                                start: s - match[0].length,
+                                name: match[0],
+                                end: s,
+                                strand: -1,
+                            }));
+                        }
+                    }
+                }
+            }
+            observer.complete();
+        });
+    }
+    freeResources() { }
+}
+exports.default = default_1;
+//# sourceMappingURL=SequenceSearchAdapter.js.map

package/dist/SequenceSearchAdapter/SequenceSearchAdapter.js.map

@@ -0,0 +1 @@
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package/dist/SequenceSearchAdapter/configSchema.d.ts

@@ -0,0 +1,2 @@
+declare const configSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+export default configSchema;

package/dist/SequenceSearchAdapter/configSchema.js

@@ -0,0 +1,28 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+const configuration_1 = require("@jbrowse/core/configuration");
+const configSchema = (0, configuration_1.ConfigurationSchema)('SequenceSearchAdapter', {
+    search: {
+        type: 'string',
+        defaultValue: '',
+        description: 'Search string or regex to search for',
+    },
+    sequenceAdapter: {
+        type: 'frozen',
+        defaultValue: null,
+    },
+    searchForward: {
+        type: 'boolean',
+        defaultValue: true,
+    },
+    searchReverse: {
+        type: 'boolean',
+        defaultValue: true,
+    },
+    caseInsensitive: {
+        type: 'boolean',
+        defaultValue: true,
+    },
+}, { explicitlyTyped: true });
+exports.default = configSchema;
+//# sourceMappingURL=configSchema.js.map

package/dist/SequenceSearchAdapter/configSchema.js.map

@@ -0,0 +1 @@
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package/dist/SequenceSearchAdapter/index.d.ts

@@ -0,0 +1,3 @@
+import PluginManager from '@jbrowse/core/PluginManager';
+declare const _default: (pluginManager: PluginManager) => void;
+export default _default;

package/dist/SequenceSearchAdapter/index.js

@@ -0,0 +1,44 @@
+"use strict";
+var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    var desc = Object.getOwnPropertyDescriptor(m, k);
+    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
+      desc = { enumerable: true, get: function() { return m[k]; } };
+    }
+    Object.defineProperty(o, k2, desc);
+}) : (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    o[k2] = m[k];
+}));
+var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
+    Object.defineProperty(o, "default", { enumerable: true, value: v });
+}) : function(o, v) {
+    o["default"] = v;
+});
+var __importStar = (this && this.__importStar) || function (mod) {
+    if (mod && mod.__esModule) return mod;
+    var result = {};
+    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
+    __setModuleDefault(result, mod);
+    return result;
+};
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+const AdapterType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/AdapterType"));
+const configSchema_1 = __importDefault(require("./configSchema"));
+exports.default = (pluginManager) => {
+    pluginManager.addAdapterType(() => new AdapterType_1.default({
+        name: 'SequenceSearchAdapter',
+        adapterMetadata: {
+            category: null,
+            hiddenFromGUI: true,
+            displayName: null,
+            description: null,
+        },
+        configSchema: configSchema_1.default,
+        getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./SequenceSearchAdapter'))).then(r => r.default),
+    }));
+};
+//# sourceMappingURL=index.js.map

package/dist/SequenceSearchAdapter/index.js.map

@@ -0,0 +1 @@
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package/dist/TwoBitAdapter/TwoBitAdapter.js

@@ -1,193 +1,85 @@
 "use strict";
-var __extends = (this && this.__extends) || (function () {
-    var extendStatics = function (d, b) {
-        extendStatics = Object.setPrototypeOf ||
-            ({ __proto__: [] } instanceof Array && function (d, b) { d.__proto__ = b; }) ||
-            function (d, b) { for (var p in b) if (Object.prototype.hasOwnProperty.call(b, p)) d[p] = b[p]; };
-        return extendStatics(d, b);
-    };
-    return function (d, b) {
-        if (typeof b !== "function" && b !== null)
-            throw new TypeError("Class extends value " + String(b) + " is not a constructor or null");
-        extendStatics(d, b);
-        function __() { this.constructor = d; }
-        d.prototype = b === null ? Object.create(b) : (__.prototype = b.prototype, new __());
-    };
-})();
-var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, P, generator) {
-    function adopt(value) { return value instanceof P ? value : new P(function (resolve) { resolve(value); }); }
-    return new (P || (P = Promise))(function (resolve, reject) {
-        function fulfilled(value) { try { step(generator.next(value)); } catch (e) { reject(e); } }
-        function rejected(value) { try { step(generator["throw"](value)); } catch (e) { reject(e); } }
-        function step(result) { result.done ? resolve(result.value) : adopt(result.value).then(fulfilled, rejected); }
-        step((generator = generator.apply(thisArg, _arguments || [])).next());
-    });
-};
-var __generator = (this && this.__generator) || function (thisArg, body) {
-    var _ = { label: 0, sent: function() { if (t[0] & 1) throw t[1]; return t[1]; }, trys: [], ops: [] }, f, y, t, g;
-    return g = { next: verb(0), "throw": verb(1), "return": verb(2) }, typeof Symbol === "function" && (g[Symbol.iterator] = function() { return this; }), g;
-    function verb(n) { return function (v) { return step([n, v]); }; }
-    function step(op) {
-        if (f) throw new TypeError("Generator is already executing.");
-        while (_) try {
-            if (f = 1, y && (t = op[0] & 2 ? y["return"] : op[0] ? y["throw"] || ((t = y["return"]) && t.call(y), 0) : y.next) && !(t = t.call(y, op[1])).done) return t;
-            if (y = 0, t) op = [op[0] & 2, t.value];
-            switch (op[0]) {
-                case 0: case 1: t = op; break;
-                case 4: _.label++; return { value: op[1], done: false };
-                case 5: _.label++; y = op[1]; op = [0]; continue;
-                case 7: op = _.ops.pop(); _.trys.pop(); continue;
-                default:
-                    if (!(t = _.trys, t = t.length > 0 && t[t.length - 1]) && (op[0] === 6 || op[0] === 2)) { _ = 0; continue; }
-                    if (op[0] === 3 && (!t || (op[1] > t[0] && op[1] < t[3]))) { _.label = op[1]; break; }
-                    if (op[0] === 6 && _.label < t[1]) { _.label = t[1]; t = op; break; }
-                    if (t && _.label < t[2]) { _.label = t[2]; _.ops.push(op); break; }
-                    if (t[2]) _.ops.pop();
-                    _.trys.pop(); continue;
-            }
-            op = body.call(thisArg, _);
-        } catch (e) { op = [6, e]; y = 0; } finally { f = t = 0; }
-        if (op[0] & 5) throw op[1]; return { value: op[0] ? op[1] : void 0, done: true };
-    }
-};
-var __read = (this && this.__read) || function (o, n) {
-    var m = typeof Symbol === "function" && o[Symbol.iterator];
-    if (!m) return o;
-    var i = m.call(o), r, ar = [], e;
-    try {
-        while ((n === void 0 || n-- > 0) && !(r = i.next()).done) ar.push(r.value);
-    }
-    catch (error) { e = { error: error }; }
-    finally {
-        try {
-            if (r && !r.done && (m = i["return"])) m.call(i);
-        }
-        finally { if (e) throw e.error; }
-    }
-    return ar;
-};
 var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-var BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
-var io_1 = require("@jbrowse/core/util/io");
-var rxjs_1 = require("@jbrowse/core/util/rxjs");
-var simpleFeature_1 = __importDefault(require("@jbrowse/core/util/simpleFeature"));
-var twobit_1 = require("@gmod/twobit");
-var configuration_1 = require("@jbrowse/core/configuration");
-var TwoBitAdapter = /** @class */ (function (_super) {
-    __extends(TwoBitAdapter, _super);
-    function TwoBitAdapter(config, getSubAdapter, pluginManager) {
-        var _this = _super.call(this, config, getSubAdapter, pluginManager) || this;
-        _this.chromSizesData = _this.initChromSizes();
-        _this.twobit = new twobit_1.TwoBitFile({
-            filehandle: (0, io_1.openLocation)((0, configuration_1.readConfObject)(config, 'twoBitLocation'), _this.pluginManager),
+const BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
+const io_1 = require("@jbrowse/core/util/io");
+const rxjs_1 = require("@jbrowse/core/util/rxjs");
+const simpleFeature_1 = __importDefault(require("@jbrowse/core/util/simpleFeature"));
+const twobit_1 = require("@gmod/twobit");
+const configuration_1 = require("@jbrowse/core/configuration");
+class TwoBitAdapter extends BaseAdapter_1.BaseSequenceAdapter {
+    constructor(config, getSubAdapter, pluginManager) {
+        super(config, getSubAdapter, pluginManager);
+        this.chromSizesData = this.initChromSizes();
+        this.twobit = new twobit_1.TwoBitFile({
+            filehandle: (0, io_1.openLocation)((0, configuration_1.readConfObject)(config, 'twoBitLocation'), this.pluginManager),
         });
-        return _this;
     }
-    TwoBitAdapter.prototype.initChromSizes = function () {
-        return __awaiter(this, void 0, void 0, function () {
-            var conf, file, data;
-            return __generator(this, function (_a) {
-                switch (_a.label) {
-                    case 0:
-                        conf = (0, configuration_1.readConfObject)(this.config, 'chromSizesLocation');
-                        if (!(conf.uri !== '/path/to/default.chrom.sizes' && conf.uri !== '')) return [3 /*break*/, 2];
-                        file = (0, io_1.openLocation)(conf, this.pluginManager);
-                        return [4 /*yield*/, file.readFile('utf8')];
-                    case 1:
-                        data = _a.sent();
-                        return [2 /*return*/, Object.fromEntries(data === null || data === void 0 ? void 0 : data.split('\n').filter(function (line) { return !!line.trim(); }).map(function (line) {
-                                var _a = __read(line.split('\t'), 2), name = _a[0], length = _a[1];
-                                return [name, +length];
-                            }))];
-                    case 2: return [2 /*return*/, undefined];
-                }
-            });
-        });
-    };
-    TwoBitAdapter.prototype.getRefNames = function () {
-        return __awaiter(this, void 0, void 0, function () {
-            var chromSizesData;
-            return __generator(this, function (_a) {
-                switch (_a.label) {
-                    case 0: return [4 /*yield*/, this.chromSizesData];
-                    case 1:
-                        chromSizesData = _a.sent();
-                        if (chromSizesData) {
-                            return [2 /*return*/, Object.keys(chromSizesData)];
-                        }
-                        return [2 /*return*/, this.twobit.getSequenceNames()];
-                }
-            });
-        });
-    };
-    TwoBitAdapter.prototype.getRegions = function () {
-        return __awaiter(this, void 0, void 0, function () {
-            var chromSizesData, refSizes;
-            return __generator(this, function (_a) {
-                switch (_a.label) {
-                    case 0: return [4 /*yield*/, this.chromSizesData];
-                    case 1:
-                        chromSizesData = _a.sent();
-                        if (chromSizesData) {
-                            return [2 /*return*/, Object.keys(chromSizesData).map(function (refName) { return ({
-                                    refName: refName,
-                                    start: 0,
-                                    end: chromSizesData[refName],
-                                }); })];
-                        }
-                        return [4 /*yield*/, this.twobit.getSequenceSizes()];
-                    case 2:
-                        refSizes = _a.sent();
-                        return [2 /*return*/, Object.keys(refSizes).map(function (refName) { return ({
-                                refName: refName,
-                                start: 0,
-                                end: refSizes[refName],
-                            }); })];
-                }
-            });
-        });
-    };
+    async initChromSizes() {
+        const conf = (0, configuration_1.readConfObject)(this.config, 'chromSizesLocation');
+        // check against default and empty in case someone makes the field blank in
+        // config editor, may want better way to check "optional config slots" in
+        // future
+        if (conf.uri !== '/path/to/default.chrom.sizes' && conf.uri !== '') {
+            const file = (0, io_1.openLocation)(conf, this.pluginManager);
+            const data = await file.readFile('utf8');
+            return Object.fromEntries(data === null || data === void 0 ? void 0 : data.split('\n').filter(line => !!line.trim()).map(line => {
+                const [name, length] = line.split('\t');
+                return [name, +length];
+            }));
+        }
+        return undefined;
+    }
+    async getRefNames() {
+        const chromSizesData = await this.chromSizesData;
+        if (chromSizesData) {
+            return Object.keys(chromSizesData);
+        }
+        return this.twobit.getSequenceNames();
+    }
+    async getRegions() {
+        const chromSizesData = await this.chromSizesData;
+        if (chromSizesData) {
+            return Object.keys(chromSizesData).map(refName => ({
+                refName,
+                start: 0,
+                end: chromSizesData[refName],
+            }));
+        }
+        const refSizes = await this.twobit.getSequenceSizes();
+        return Object.keys(refSizes).map(refName => ({
+            refName,
+            start: 0,
+            end: refSizes[refName],
+        }));
+    }
     /**
      * Fetch features for a certain region
      * @param param -
      * @returns Observable of Feature objects in the region
      */
-    TwoBitAdapter.prototype.getFeatures = function (_a) {
-        var _this = this;
-        var refName = _a.refName, start = _a.start, end = _a.end;
-        return (0, rxjs_1.ObservableCreate)(function (observer) { return __awaiter(_this, void 0, void 0, function () {
-            var size, regionEnd, seq;
-            return __generator(this, function (_a) {
-                switch (_a.label) {
-                    case 0: return [4 /*yield*/, this.twobit.getSequenceSize(refName)];
-                    case 1:
-                        size = _a.sent();
-                        regionEnd = size !== undefined ? Math.min(size, end) : end;
-                        return [4 /*yield*/, this.twobit.getSequence(refName, start, regionEnd)];
-                    case 2:
-                        seq = _a.sent();
-                        if (seq) {
-                            observer.next(new simpleFeature_1.default({
-                                id: "".concat(refName, " ").concat(start, "-").concat(regionEnd),
-                                data: { refName: refName, start: start, end: regionEnd, seq: seq },
-                            }));
-                        }
-                        observer.complete();
-                        return [2 /*return*/];
-                }
-            });
-        }); });
-    };
+    getFeatures({ refName, start, end }) {
+        return (0, rxjs_1.ObservableCreate)(async (observer) => {
+            const size = await this.twobit.getSequenceSize(refName);
+            const regionEnd = size !== undefined ? Math.min(size, end) : end;
+            const seq = await this.twobit.getSequence(refName, start, regionEnd);
+            if (seq) {
+                observer.next(new simpleFeature_1.default({
+                    id: `${refName} ${start}-${regionEnd}`,
+                    data: { refName, start, end: regionEnd, seq },
+                }));
+            }
+            observer.complete();
+        });
+    }
     /**
      * called to provide a hint that data tied to a certain region
      * will not be needed for the forseeable future and can be purged
      * from caches, etc
      */
-    TwoBitAdapter.prototype.freeResources = function ( /* { region } */) { };
-    return TwoBitAdapter;
-}(BaseAdapter_1.BaseSequenceAdapter));
+    freeResources( /* { region } */) { }
+}
 exports.default = TwoBitAdapter;
 //# sourceMappingURL=TwoBitAdapter.js.map

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package/dist/TwoBitAdapter/configSchema.js

@@ -1,6 +1,6 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-var configuration_1 = require("@jbrowse/core/configuration");
+const configuration_1 = require("@jbrowse/core/configuration");
 exports.default = (0, configuration_1.ConfigurationSchema)('TwoBitAdapter', {
     twoBitLocation: {
         type: 'fileLocation',

package/dist/TwoBitAdapter/configSchema.js.map

@@ -1 +1 @@
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+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/TwoBitAdapter/configSchema.ts"],"names":[],"mappings":";;AAAA,+DAAiE;AAEjE,kBAAe,IAAA,mCAAmB,EAChC,eAAe,EACf;IACE,cAAc,EAAE;QACd,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE,EAAE,GAAG,EAAE,kBAAkB,EAAE,YAAY,EAAE,aAAa,EAAE;KACvE;IACD,kBAAkB,EAAE;QAClB,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE;YACZ,GAAG,EAAE,8BAA8B;YACnC,YAAY,EAAE,aAAa;SAC5B;QACD,WAAW,EACT,8GAA8G;KACjH;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA"}

package/dist/TwoBitAdapter/index.d.ts

@@ -1 +1,3 @@
-export { default as configSchema } from './configSchema';
+import PluginManager from '@jbrowse/core/PluginManager';
+declare const _default: (pluginManager: PluginManager) => void;
+export default _default;